According to a Cambridge University study, eight in 10 classrooms in England are fitted with immoderate bright and flickering lights, which, according to experts, result in eye strain and loss of concentration.
The study authors say that the problem has been intensified by the use of computerized whiteboards and poor classroom design.
"The installation of whiteboards and data projectors in classrooms has been enormous over the last 10 years - I would be amazed if they were not now used in every school in the country," the Telegraph quoted Mark Winterbottom, from Cambridge's faculty of education, as saying.
"There is evidence that this equipment, coupled with excessive fluorescent and natural light, can cause headaches and impair visual performance," he added.
For the study, Dr Winterbottom and Professor Arnold Wilkins, from Essex University, investigated the lights in 90 classrooms at 11 secondaries. The results of their assessment showed that 100Hz fluorescent lighting, which creates an "imperceptible flicker that can cause visual discomfort and make it more difficult to read accurately", had been installed in nearly 80 per cent of rooms.
The study said that problem was further worsened by whiteboards and failure to control the natural light levels, because of poor classroom designs or faulty blinds. The Government has spent an estimated 50 million pounds on "interactive whiteboards'', which use video, animation, graphics and sound.
Researchers said that nine in 10 classrooms were "excessively bright". Dr Winterbottom said that schools should fully utilise natural daylight, and use high frequency 32KHz lighting which "does not cause discomfort".
A spokesman for the Department for Children, Schools and Families said hat schools should be aware of the safety issues, adding that information about the use of electronic whiteboards and lighting was openly available.